CA2884246C - Pyrosequencage multiplexe a l'aide d'etiquettes d'identification de polynucleotide anti-bruit, non interferentes - Google Patents
Pyrosequencage multiplexe a l'aide d'etiquettes d'identification de polynucleotide anti-bruit, non interferentes Download PDFInfo
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- CA2884246C CA2884246C CA2884246A CA2884246A CA2884246C CA 2884246 C CA2884246 C CA 2884246C CA 2884246 A CA2884246 A CA 2884246A CA 2884246 A CA2884246 A CA 2884246A CA 2884246 C CA2884246 C CA 2884246C
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- 108091033319 polynucleotide Proteins 0.000 title claims abstract description 106
- 102000040430 polynucleotide Human genes 0.000 title claims abstract description 106
- 239000002157 polynucleotide Substances 0.000 title claims abstract description 106
- 230000002452 interceptive effect Effects 0.000 title claims abstract description 33
- 238000012175 pyrosequencing Methods 0.000 title claims abstract description 29
- 238000000034 method Methods 0.000 claims abstract description 58
- 230000003321 amplification Effects 0.000 claims abstract description 39
- 238000003199 nucleic acid amplification method Methods 0.000 claims abstract description 39
- 230000002596 correlated effect Effects 0.000 claims abstract description 5
- 238000006243 chemical reaction Methods 0.000 claims description 27
- 102000039446 nucleic acids Human genes 0.000 claims description 19
- 108020004707 nucleic acids Proteins 0.000 claims description 19
- 150000007523 nucleic acids Chemical class 0.000 claims description 19
- 238000003757 reverse transcription PCR Methods 0.000 claims description 7
- FWMNVWWHGCHHJJ-SKKKGAJSSA-N 4-amino-1-[(2r)-6-amino-2-[[(2r)-2-[[(2r)-2-[[(2r)-2-amino-3-phenylpropanoyl]amino]-3-phenylpropanoyl]amino]-4-methylpentanoyl]amino]hexanoyl]piperidine-4-carboxylic acid Chemical compound C([C@H](C(=O)N[C@H](CC(C)C)C(=O)N[C@H](CCCCN)C(=O)N1CCC(N)(CC1)C(O)=O)NC(=O)[C@H](N)CC=1C=CC=CC=1)C1=CC=CC=C1 FWMNVWWHGCHHJJ-SKKKGAJSSA-N 0.000 claims description 6
- 230000001580 bacterial effect Effects 0.000 claims description 6
- 230000002538 fungal effect Effects 0.000 claims description 5
- 230000003612 virological effect Effects 0.000 claims description 5
- 241001465754 Metazoa Species 0.000 claims description 4
- 238000009396 hybridization Methods 0.000 claims description 3
- 238000003752 polymerase chain reaction Methods 0.000 description 16
- 108020004414 DNA Proteins 0.000 description 13
- 238000012163 sequencing technique Methods 0.000 description 13
- 239000002773 nucleotide Substances 0.000 description 12
- 125000003729 nucleotide group Chemical group 0.000 description 12
- 238000001514 detection method Methods 0.000 description 9
- 238000007403 mPCR Methods 0.000 description 9
- 108091093088 Amplicon Proteins 0.000 description 6
- 108090000790 Enzymes Proteins 0.000 description 6
- 102000004190 Enzymes Human genes 0.000 description 6
- 238000004458 analytical method Methods 0.000 description 6
- XPPKVPWEQAFLFU-UHFFFAOYSA-J diphosphate(4-) Chemical compound [O-]P([O-])(=O)OP([O-])([O-])=O XPPKVPWEQAFLFU-UHFFFAOYSA-J 0.000 description 4
- 235000011180 diphosphates Nutrition 0.000 description 4
- 201000010099 disease Diseases 0.000 description 3
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 3
- 238000010348 incorporation Methods 0.000 description 3
- 239000000872 buffer Substances 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 230000003247 decreasing effect Effects 0.000 description 2
- 238000002405 diagnostic procedure Methods 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 230000007613 environmental effect Effects 0.000 description 2
- 230000002194 synthesizing effect Effects 0.000 description 2
- 230000004544 DNA amplification Effects 0.000 description 1
- 230000006820 DNA synthesis Effects 0.000 description 1
- 208000026350 Inborn Genetic disease Diseases 0.000 description 1
- 108060001084 Luciferase Proteins 0.000 description 1
- 239000005089 Luciferase Substances 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 238000003556 assay Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 238000003759 clinical diagnosis Methods 0.000 description 1
- 230000000295 complement effect Effects 0.000 description 1
- 238000011109 contamination Methods 0.000 description 1
- 230000000875 corresponding effect Effects 0.000 description 1
- 230000023077 detection of light stimulus Effects 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 238000003745 diagnosis Methods 0.000 description 1
- 231100000676 disease causative agent Toxicity 0.000 description 1
- 230000002255 enzymatic effect Effects 0.000 description 1
- 238000006911 enzymatic reaction Methods 0.000 description 1
- 208000016361 genetic disease Diseases 0.000 description 1
- 208000015181 infectious disease Diseases 0.000 description 1
- 244000005700 microbiome Species 0.000 description 1
- 238000001668 nucleic acid synthesis Methods 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 238000004445 quantitative analysis Methods 0.000 description 1
- 239000000376 reactant Substances 0.000 description 1
- 239000011541 reaction mixture Substances 0.000 description 1
- 238000005070 sampling Methods 0.000 description 1
- 238000000926 separation method Methods 0.000 description 1
- 241000894007 species Species 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- 238000012360 testing method Methods 0.000 description 1
Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
- C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
- C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
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- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Immunology (AREA)
- Analytical Chemistry (AREA)
- General Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biotechnology (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Cell Biology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
La présente invention concerne en général un procédé multiplexe pour l'analyse d'échantillons, comprenant l'utilisation de l'amplification polynucléotidique pour produire des produits amplifiés où une ou plusieurs séquences cibles sont marquées par une étiquette d'identification de polynucléotide spécifique d'une cible non-annulation non-interférente, le pyroséquençage des produits amplifiés par l'intermédiaire de la séquence d'étiquette d'identification de polynucléotide spécifique d'une cible non-annulation pour détecter la présence d'une ou plusieurs étiquettes d'identification de polynucléotide spécifiques. La présence d'une étiquette d'identification de polynucléotide spécifique étant corrélée à la présence d'une séquence cible spécifique.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201261705089P | 2012-09-24 | 2012-09-24 | |
| US61/705,089 | 2012-09-24 | ||
| PCT/US2013/061460 WO2014047646A1 (fr) | 2012-09-24 | 2013-09-24 | Pyroséquençage multiplexe à l'aide d'étiquettes d'identification de polynucléotide anti-bruit, non interférentes |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2884246A1 CA2884246A1 (fr) | 2014-03-27 |
| CA2884246C true CA2884246C (fr) | 2023-11-07 |
Family
ID=50342014
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2884246A Active CA2884246C (fr) | 2012-09-24 | 2013-09-24 | Pyrosequencage multiplexe a l'aide d'etiquettes d'identification de polynucleotide anti-bruit, non interferentes |
Country Status (7)
| Country | Link |
|---|---|
| US (1) | US9938578B2 (fr) |
| JP (2) | JP2015530096A (fr) |
| CN (2) | CN114085896A (fr) |
| CA (1) | CA2884246C (fr) |
| DE (1) | DE112013004650T5 (fr) |
| GB (1) | GB2521570B (fr) |
| WO (1) | WO2014047646A1 (fr) |
Families Citing this family (28)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US8748103B2 (en) | 2008-11-07 | 2014-06-10 | Sequenta, Inc. | Monitoring health and disease status using clonotype profiles |
| US9528160B2 (en) | 2008-11-07 | 2016-12-27 | Adaptive Biotechnolgies Corp. | Rare clonotypes and uses thereof |
| US8628927B2 (en) | 2008-11-07 | 2014-01-14 | Sequenta, Inc. | Monitoring health and disease status using clonotype profiles |
| US9506119B2 (en) | 2008-11-07 | 2016-11-29 | Adaptive Biotechnologies Corp. | Method of sequence determination using sequence tags |
| US9365901B2 (en) | 2008-11-07 | 2016-06-14 | Adaptive Biotechnologies Corp. | Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia |
| EP2364368B1 (fr) | 2008-11-07 | 2014-01-15 | Sequenta, Inc. | Procédés de surveillance de maladies par analyse de séquence |
| DK2387627T3 (en) | 2009-01-15 | 2016-07-04 | Adaptive Biotechnologies Corp | Adaptive immunity profiling and methods for producing monoclonal antibodies |
| EP2446052B1 (fr) | 2009-06-25 | 2018-08-08 | Fred Hutchinson Cancer Research Center | Procédé de mesure de l'immunité adaptative |
| US10385475B2 (en) | 2011-09-12 | 2019-08-20 | Adaptive Biotechnologies Corp. | Random array sequencing of low-complexity libraries |
| US9279159B2 (en) | 2011-10-21 | 2016-03-08 | Adaptive Biotechnologies Corporation | Quantification of adaptive immune cell genomes in a complex mixture of cells |
| CA2858070C (fr) | 2011-12-09 | 2018-07-10 | Adaptive Biotechnologies Corporation | Diagnostic des malignites lymphoides et detection de maladie residuelle minimale |
| US9499865B2 (en) | 2011-12-13 | 2016-11-22 | Adaptive Biotechnologies Corp. | Detection and measurement of tissue-infiltrating lymphocytes |
| DK2823060T3 (en) | 2012-03-05 | 2018-05-28 | Adaptive Biotechnologies Corp | Determination of associated immune receptor chains from frequency-matched subunits |
| ES2582554T3 (es) | 2012-05-08 | 2016-09-13 | Adaptive Biotechnologies Corporation | Composiciones y método para medir y calibrar el sesgo de la amplificación en reacciones de PCR multiplexadas |
| DK2904111T3 (en) | 2012-10-01 | 2018-03-12 | Adaptive Biotechnologies Corp | Immune competence evaluation of adaptive immune receptor diversity and clonality characterization |
| US9708657B2 (en) | 2013-07-01 | 2017-07-18 | Adaptive Biotechnologies Corp. | Method for generating clonotype profiles using sequence tags |
| AU2015227054A1 (en) | 2014-03-05 | 2016-09-22 | Adaptive Biotechnologies Corporation | Methods using randomer-containing synthetic molecules |
| US10066265B2 (en) | 2014-04-01 | 2018-09-04 | Adaptive Biotechnologies Corp. | Determining antigen-specific t-cells |
| EP3132059B1 (fr) | 2014-04-17 | 2020-01-08 | Adaptive Biotechnologies Corporation | Quantification de génomes de cellules de l'immunité acquise dans un mélange complexe de cellules |
| ES2784343T3 (es) | 2014-10-29 | 2020-09-24 | Adaptive Biotechnologies Corp | Detección simultánea altamente multiplexada de ácidos nucleicos que codifican heterodímeros de receptores inmunes adaptativos emparejados de muchas muestras |
| US10246701B2 (en) | 2014-11-14 | 2019-04-02 | Adaptive Biotechnologies Corp. | Multiplexed digital quantitation of rearranged lymphoid receptors in a complex mixture |
| AU2015353581A1 (en) | 2014-11-25 | 2017-06-15 | Adaptive Biotechnologies Corporation | Characterization of adaptive immune response to vaccination or infection using immune repertoire sequencing |
| EP3262196B1 (fr) | 2015-02-24 | 2020-12-09 | Adaptive Biotechnologies Corp. | Méthode pour la détermination du statut hla à l'aide du séquençage du répertoire immunitaire |
| EP3277294B1 (fr) | 2015-04-01 | 2024-05-15 | Adaptive Biotechnologies Corp. | Procédé d'identification des récepteurs de lymphocytes t spécifiques à compatibilité humaine pour une cible antigénique |
| AU2016289369B2 (en) * | 2015-07-07 | 2020-07-02 | Pillar Biosciences Inc. | Method for reducing primer-dimer amplification |
| US10428325B1 (en) | 2016-09-21 | 2019-10-01 | Adaptive Biotechnologies Corporation | Identification of antigen-specific B cell receptors |
| US11254980B1 (en) | 2017-11-29 | 2022-02-22 | Adaptive Biotechnologies Corporation | Methods of profiling targeted polynucleotides while mitigating sequencing depth requirements |
| US20220112557A1 (en) | 2019-01-10 | 2022-04-14 | Iovance Biotherapeutics, Inc. | System and methods for monitoring adoptive cell therapy clonality and persistence |
Family Cites Families (11)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP1534859B1 (fr) * | 2002-06-28 | 2010-11-24 | PrimeraDx, Inc. | Methodes de detection de polymorphismes genetiques |
| JP4770163B2 (ja) * | 2004-12-03 | 2011-09-14 | 大日本印刷株式会社 | 生物情報の解析装置および圧縮装置 |
| US20090087840A1 (en) | 2006-05-19 | 2009-04-02 | Codon Devices, Inc. | Combined extension and ligation for nucleic acid assembly |
| CA2701411A1 (fr) * | 2007-10-16 | 2009-04-23 | F. Hoffmann-La Roche Ag | Genotypage hla a haute resolution et haut debit par sequencage clonal |
| US10150990B2 (en) * | 2008-04-21 | 2018-12-11 | Roche Molecular Systems, Inc. | Ribonucleotide tag nucleic acid detection |
| US8586310B2 (en) * | 2008-09-05 | 2013-11-19 | Washington University | Method for multiplexed nucleic acid patch polymerase chain reaction |
| WO2010082815A1 (fr) * | 2009-01-13 | 2010-07-22 | Keygene N.V. | Nouvelles stratégies de séquençage du génome |
| DK2414547T3 (da) * | 2009-04-02 | 2014-06-16 | Fluidigm Corp | Multiprimer-amplifikationsmetode til stregkodning af målnukleinsyrer |
| US20110257031A1 (en) * | 2010-02-12 | 2011-10-20 | Life Technologies Corporation | Nucleic acid, biomolecule and polymer identifier codes |
| WO2011155833A2 (fr) * | 2010-06-09 | 2011-12-15 | Keygene N.V. | Code-barres de séquences combinatoires pour criblage à haut débit |
| ES2731460T3 (es) * | 2010-10-08 | 2019-11-15 | Harvard College | Alto rendimiento de células individuales con código de barra |
-
2013
- 2013-09-24 DE DE112013004650.4T patent/DE112013004650T5/de active Pending
- 2013-09-24 GB GB1506772.1A patent/GB2521570B/en active Active
- 2013-09-24 WO PCT/US2013/061460 patent/WO2014047646A1/fr active Application Filing
- 2013-09-24 CN CN202111317841.1A patent/CN114085896A/zh active Pending
- 2013-09-24 CA CA2884246A patent/CA2884246C/fr active Active
- 2013-09-24 US US14/035,686 patent/US9938578B2/en active Active
- 2013-09-24 CN CN201380047883.5A patent/CN104685062A/zh active Pending
- 2013-09-24 JP JP2015533282A patent/JP2015530096A/ja active Pending
-
2019
- 2019-07-26 JP JP2019137662A patent/JP7110155B2/ja active Active
Also Published As
| Publication number | Publication date |
|---|---|
| JP2015530096A (ja) | 2015-10-15 |
| CN104685062A (zh) | 2015-06-03 |
| US9938578B2 (en) | 2018-04-10 |
| CN114085896A (zh) | 2022-02-25 |
| US20140094376A1 (en) | 2014-04-03 |
| GB2521570A (en) | 2015-06-24 |
| WO2014047646A9 (fr) | 2014-06-19 |
| CA2884246A1 (fr) | 2014-03-27 |
| JP7110155B2 (ja) | 2022-08-01 |
| JP2019201658A (ja) | 2019-11-28 |
| WO2014047646A1 (fr) | 2014-03-27 |
| GB201506772D0 (en) | 2015-06-03 |
| DE112013004650T5 (de) | 2015-06-18 |
| GB2521570B (en) | 2021-01-06 |
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